Organic by-products (OB) can provide nutrition to energy crops but there is a potential risk of pollution to soil, groundwater (GW) and surface water (SW). A mass-balance inventory for two energy crops spread with biosolids (BS) and distillery effluent (DE) was created in order to study the fate of nutrients. Biosolids and distillery effluent (DE) were spread on both Miscanthus x giganteus and short rotation coppice willow (SRCW). Applications were conducted at rates of 100%, 50% and 0% (control) of permissible P loads. Losses of nutrients (N,P) and heavy metals (Cd, Cu, Cr, Pb, Ni, and Zn) to groundwater and overland flow (OLF), and crop uptake were determined. Total inputs (from soil, OB amendment and atmospheric deposition) and losses were calculated and compared. The greatest input was from the soil, the smallest input was atmospheric deposition. The largest output was crop off-take; the smallest was loss to OLF. Elemental uptake by Miscanthus was lower than that of willow but losses to groundwater and overland flow was similar for both crops. This study has shown that organic byproducts can be used to enhance the nutrition of energy crops without deleterious environmental consequences.